Michael Matheson told The Scotsman that a lack of ministerial oversight over how Network Rail operated north of the Border was partly to blame for the misery many passengers have endured in recent months.
ScotRail, which operates the vast majority of passenger services in Scotland, has already been forced to apologise to customers for problems with repeated cancellations and staff shortages.
The franchise, which is operated by Abellio, has been warned by Mr Matheson that if it fails to meet all aspects of a remedial plan put in place it could be in breach of contract.
But the MSP claimed the blame for recent issues was not ScotRail’s alone.
“I’m increasingly of the view that the structural arrangements don’t work,” he said in an interview ahead of this weekend’s SNP conference.
“I don’t think franchising is the most appropriate way of delivering railway services. The way we operate Network Rail and the franchise arrangement separate from one another no longer serves the travelling public well. That needs to change.
“Some of the problems within the rail network, I think, are symptomatic of existing structural arrangements.”
Mr Matheson added he had made recommendations to that effect to the Williams Rail Review, which was established by the UK government to examine all aspects of the network and make recommendations for their improvement.
He continued: “I thought it was summed up well recently by Tom Harris, a former transport minister in Tony Blair’s Government, who said why would you have Highways England running the trunk road network in Scotland?
“Well, why would you have Network Rail running the network here in Scotland from Milton Keynes?
“Part of the challenge has been, historically, the rail network in Scotland has been treated as a region - but it’s a national network. It needs to be treated that way.
“It’s not just about the devolution of Network Rail, We can set objectives, we can give them money, but we can’t hold them to account.
“The other area I would like to see change is in the way franchising operates. It has evolved over decades. “It’s got to the point I think it’s no longer sustainable. It has to become better integrated.”\ Scottish Labour has attempted to capitalise on passenger unhappiness with transport services in recent months, with Richard Leonard calling for “universal free bus travel”.
The party has also previously attempted to have Abellio’s franchise contract ended early.
“We don’t have the powers to nationalise the rail network in Scotland,” said Mr Matheson, in reference to a pledge by Labour to bring the system into public ownership.
“It’s a matter reserved to the UK government. I have called on Labour repeatedly to support us in seeing the full devolution of the rail network, but also to have wider powers in how we run our rail network. To date, I’m still waiting for them to get behind us on supporting that.
Mr Matheson added that extending free bus passes to all Scots up to the age of 25 could cost £230 million a year.
“I have no idea where Labour has got their figures from. But I suspect it was written on the back of a bus ticket,” he added.